Contacts of the strand formed by residues 320 - 331 (chain B) in PDB entry 4Y2H
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLN 320 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B VAL 3.7 0.3 - - - +
238B VAL* 3.3 8.8 - - - +
239B GLN 3.0 32.5 + - - +
240B GLY* 3.6 2.3 - - - -
241B LEU* 2.7 38.8 + - - +
289B ALA* 4.3 5.6 - - + -
290B ILE 3.8 7.2 - - - +
291B TRP* 4.0 16.8 - - + -
309B THR 2.8 27.0 + - - +
310B SER 3.6 2.0 + - - -
311B PRO* 3.4 32.0 - - + +
315B ALA* 6.1 2.8 - - - +
318B TRP 4.0 3.6 - - - -
319B LYS* 1.3 90.5 + - - +
321B ALA* 1.3 61.2 + - - +
322B LEU* 4.0 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B TYR* 5.0 3.6 - - + -
160B GLY* 4.1 20.6 - - - +
236B ILE* 3.7 19.7 - - + -
237B VAL 3.6 3.8 - - - -
238B VAL* 4.8 2.2 - - + +
288B PHE 3.9 0.2 - - - +
289B ALA* 3.4 1.7 - - - -
290B ILE* 2.8 58.9 + - + +
320B GLN* 1.3 74.3 - - - +
322B LEU* 1.3 61.9 + - - +
323B LEU* 4.0 2.2 + - - +
353B LEU* 5.8 0.2 - - + -
373B MET* 5.2 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B ILE* 4.5 4.3 - - + -
198B ASP* 3.4 14.8 - - + +
235B GLU 4.2 1.2 - - - +
236B ILE* 3.6 8.3 - - - +
237B VAL* 2.7 40.8 + - + +
239B GLN* 3.6 32.8 - - + +
241B LEU* 3.7 35.0 - - + -
288B PHE 3.5 5.6 - - - +
289B ALA* 3.7 13.2 - - + -
320B GLN* 4.0 4.0 - - + -
321B ALA* 1.3 78.3 - - - +
323B LEU* 1.3 61.9 + - - +
324B TYR* 3.4 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B ILE* 3.9 22.0 - - + -
287B GLY* 3.2 3.6 - - - -
288B PHE* 2.8 46.4 + - + +
290B ILE* 4.2 13.0 - - + -
321B ALA 4.6 5.6 - - - +
322B LEU* 1.3 79.3 - - - +
324B TYR* 1.3 63.6 + - - +
325B LEU* 3.7 0.7 + - - +
341B ILE* 3.9 17.0 - - + -
355B VAL* 3.8 28.0 - - + -
357B LEU* 4.5 15.2 - - + +
371B PHE* 3.8 37.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B ILE* 4.9 3.1 - - + -
198B ASP* 2.7 30.8 + - + -
201B LEU* 3.6 31.6 - - + +
230B LEU 3.9 20.4 - - - -
231B MET* 4.2 11.7 - - + +
233B HIS* 3.9 14.4 - + + +
235B GLU 5.3 1.0 + - - -
237B VAL* 3.9 29.4 - - + +
239B GLN* 4.2 4.5 + - - -
286B HIS* 3.4 17.5 - - + +
287B GLY* 5.1 0.4 - - - -
322B LEU* 3.4 27.1 + - + +
323B LEU* 1.3 73.3 - - - +
325B LEU* 1.3 64.1 + - - +
369B LYS* 2.7 29.7 + - - +
371B PHE* 3.4 17.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B MET* 3.2 21.0 - - - +
285B MET* 4.0 31.2 - - + +
286B HIS 2.9 15.6 + - - +
287B GLY* 3.6 12.6 - - - -
288B PHE* 3.8 17.0 - - + -
323B LEU 4.7 0.2 - - - +
324B TYR* 1.3 77.5 - - - +
326B ASN* 1.3 65.7 + - - +
327B GLU* 3.2 13.0 - - - +
329B VAL* 3.6 29.4 - - + -
357B LEU* 5.1 1.8 - - + -
359B TYR* 3.5 43.3 - - + +
361B VAL* 4.7 2.0 - - + -
369B LYS* 3.9 3.4 - - - +
371B PHE* 6.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B THR* 3.7 8.3 - - - +
228B ARG* 5.1 1.0 - - - -
231B MET* 3.3 22.7 - - - +
232B GLY* 3.8 17.2 + - - +
325B LEU* 1.3 72.8 - - - +
327B GLU* 1.3 80.2 + - - +
359B TYR* 4.8 5.3 + - - +
369B LYS* 3.0 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B THR* 3.8 11.4 - - + -
231B MET* 3.5 7.1 - - - +
325B LEU* 3.2 20.9 - - - +
326B ASN* 1.3 96.4 + - - +
328B PRO* 1.3 84.6 - - + +
329B VAL* 3.8 7.6 + - + +
359B TYR* 5.5 2.3 + - - -
364B GLN* 5.8 0.3 + - - -
367B LYS* 4.3 16.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LEU* 3.9 16.4 - - + -
227B THR* 4.0 9.4 - - + +
231B MET* 3.8 19.7 - - + -
284B PRO* 5.1 8.7 - - + -
285B MET 3.4 9.0 - - - +
286B HIS* 4.0 16.6 - - + +
327B GLU* 1.3 99.0 - - + +
329B VAL* 1.3 62.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B PRO* 4.6 1.6 - - - -
285B MET* 2.6 46.0 + - + +
325B LEU* 3.6 27.4 - - + -
327B GLU* 4.0 8.3 - - + +
328B PRO* 1.3 80.5 - - - +
330B GLN* 1.3 71.2 + - - +
361B VAL* 4.4 19.5 - - + +
364B GLN* 3.9 29.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B SER* 3.9 10.3 - - - -
283B ALA* 3.2 36.4 + - - +
284B PRO* 3.7 16.5 - - - +
328B PRO 4.3 0.2 - - - -
329B VAL* 1.3 82.5 - - - +
331B VAL* 1.3 60.6 + - - +
332B GLU* 3.7 17.9 + - - +
335B THR* 5.7 0.3 - - - +
361B VAL* 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B LEU* 4.4 17.7 - - + -
279B CYS* 3.8 21.1 - - + -
281B GLY 3.8 11.4 - - - +
282B SER* 3.2 3.8 - - - -
283B ALA* 2.9 38.3 + - + +
285B MET* 4.0 20.4 - - + -
329B VAL 3.5 1.7 + - - +
330B GLN* 1.3 77.9 + - - +
332B GLU* 1.3 70.6 + - - +
335B THR* 3.7 16.8 - - + +
361B VAL* 3.7 28.9 - - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il